Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015498.1 Corchorus capsularis cultivar CVL-1 contig15519, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 42125
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:12458 original size:2 final size:2
Alignment explanation
Indices: 12451--12484 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12441 AGATTTAGAT
12451 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12485 ATCTAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12507 original size:18 final size:20
Alignment explanation
Indices: 12484--12553 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
12474 ATATATATAT
12484 AATCTA-AAA-AAAAAAGTA
1 AATCTAGAAATAAAAAAGTA
12502 AATCTAGAAATAAAAATAGT-
1 AATCTAGAAATAAAAA-AGTA
12522 -A---AGAAA-AAAAAAGTA
1 AATCTAGAAATAAAAAAGTA
12537 AATCTAGAAATAAAAAA
1 AATCTAGAAATAAAAAA
12554 AAAGTAGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
14 3 0.07
15 5 0.12
16 6 0.14
18 6 0.14
19 9 0.21
20 11 0.26
21 3 0.07
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.17
Consensus pattern (20 bp):
AATCTAGAAATAAAAAAGTA
Found at i:12536 original size:35 final size:37
Alignment explanation
Indices: 12490--12570 Score: 130
Period size: 35 Copynumber: 2.2 Consensus size: 37
12480 ATATAATCTA
*
12490 AAAAAAAAAGTAAATCTAGAAAT-AAAAATAGTA-AG
1 AAAAAAAAAGTAAATCTAGAAATAAAAAAAAGTAGAG
12525 AAAAAAAAAGTAAATCTAGAAATAAAAAAAAAGTAGAG
1 AAAAAAAAAGTAAATCTAGAAAT-AAAAAAAAGTAGAG
12563 AAAAAAAA
1 AAAAAAAA
12571 CTTTGGTTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
35 23 0.55
37 9 0.21
38 10 0.24
ACGTcount: A:0.73, C:0.02, G:0.11, T:0.14
Consensus pattern (37 bp):
AAAAAAAAAGTAAATCTAGAAATAAAAAAAAGTAGAG
Found at i:12538 original size:23 final size:23
Alignment explanation
Indices: 12512--12559 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
12502 AATCTAGAAA
*
12512 TAAAAATAGTAAGAAAAAAAAAG
1 TAAAAATAGAAAGAAAAAAAAAG
** *
12535 TAAATCTAGAAATAAAAAAAAAG
1 TAAAAATAGAAAGAAAAAAAAAG
12558 TA
1 TA
12560 GAGAAAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (23 bp):
TAAAAATAGAAAGAAAAAAAAAG
Found at i:13057 original size:22 final size:21
Alignment explanation
Indices: 13001--13057 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
12991 TTAGTTTAGT
* *
13001 TTGGGCTTTAATGTTTTCCGT
1 TTGGGCTTTAATGTTTTCAGG
13022 TTGGGACTTGTAAT-TTTTGCAAGG
1 TTGGG-CTT-TAATGTTTT-C-AGG
13046 TTGGGCTTTAAT
1 TTGGGCTTTAAT
13058 ATACATATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 5 0.17
22 11 0.37
23 8 0.27
24 6 0.20
ACGTcount: A:0.16, C:0.11, G:0.26, T:0.47
Consensus pattern (21 bp):
TTGGGCTTTAATGTTTTCAGG
Found at i:13751 original size:10 final size:10
Alignment explanation
Indices: 13736--13762 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
13726 TTTCCAAGAT
13736 AAAAAAAAAG
1 AAAAAAAAAG
13746 AAAAAAAAAG
1 AAAAAAAAAG
13756 AAAAAAA
1 AAAAAAA
13763 TGAGTCTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:13879 original size:53 final size:53
Alignment explanation
Indices: 13822--13933 Score: 145
Period size: 52 Copynumber: 2.1 Consensus size: 53
13812 CAAATCAAAA
* ** *
13822 TTCAAAAATAAAAAATTTTTCATCAAGTTTTCAAAGTATTCAATTTAGGTCTT
1 TTCAAAAATAAAAAAGTTCCCATCAAATTTTCAAAGTATTCAATTTAGGTCTT
* ** *
13875 TTC-AAATTAGGAAAGTTCCCATCAAATTTTCAAAGTGTTCAATTTAGGTCTT
1 TTCAAAAATAAAAAAGTTCCCATCAAATTTTCAAAGTATTCAATTTAGGTCTT
13927 TTCAAAA
1 TTCAAAA
13934 CATTCAAAGA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
52 44 0.88
53 6 0.12
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (53 bp):
TTCAAAAATAAAAAAGTTCCCATCAAATTTTCAAAGTATTCAATTTAGGTCTT
Found at i:14698 original size:16 final size:16
Alignment explanation
Indices: 14674--14706 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
14664 GAATGATCCT
*
14674 ACAATGAAAGTGGAAG
1 ACAAAGAAAGTGGAAG
14690 ACAAAGAAAGTGGAAG
1 ACAAAGAAAGTGGAAG
14706 A
1 A
14707 TGAGTACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.30, T:0.09
Consensus pattern (16 bp):
ACAAAGAAAGTGGAAG
Found at i:15740 original size:11 final size:11
Alignment explanation
Indices: 15726--15751 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
15716 AATATTTATT
15726 GCCATGTCATA
1 GCCATGTCATA
15737 GCCATGTCATA
1 GCCATGTCATA
15748 GCCA
1 GCCA
15752 CGTTACACAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (11 bp):
GCCATGTCATA
Found at i:16047 original size:31 final size:31
Alignment explanation
Indices: 15990--16051 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
15980 TATAGTATAT
* ** *
15990 GTATTTTATTTTTACTTAGTATAAAAAAAAA
1 GTATTTTATTTTTACTGAAAAAAAAAAAAAA
16021 GTATTTTATTTTTACTGAAAAAAAAAAAAAA
1 GTATTTTATTTTTACTGAAAAAAAAAAAAAA
16052 CCCGGTAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.40
Consensus pattern (31 bp):
GTATTTTATTTTTACTGAAAAAAAAAAAAAA
Found at i:26694 original size:24 final size:23
Alignment explanation
Indices: 26650--26698 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
26640 CTAGTAGTTG
* *
26650 ATATATATATTAATATAGATAGAT
1 ATATAAATAATAATATAGATA-AT
26674 ATATAAATAATAATA-AGGATAAT
1 ATATAAATAATAATATA-GATAAT
26697 AT
1 AT
26699 TGTAACAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (23 bp):
ATATAAATAATAATATAGATAAT
Found at i:30377 original size:13 final size:13
Alignment explanation
Indices: 30359--30383 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30349 ATTGATTCAA
30359 TTTTTTTTTTAAT
1 TTTTTTTTTTAAT
30372 TTTTTTTTTTAA
1 TTTTTTTTTTAA
30384 CTTAACAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTTTTAAT
Found at i:33478 original size:16 final size:15
Alignment explanation
Indices: 33440--33493 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
33430 TCGGAACCAT
33440 ATGACCTGAAACCGAAA
1 ATGACCTG-AACC-AAA
*
33457 AAGACCTGAACCAAA
1 ATGACCTGAACCAAA
* *
33472 ATTGACCCGAACCCAA
1 A-TGACCTGAACCAAA
33488 ATGACC
1 ATGACC
33494 CGGCATTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 9 0.28
16 16 0.50
17 7 0.22
ACGTcount: A:0.44, C:0.30, G:0.15, T:0.11
Consensus pattern (15 bp):
ATGACCTGAACCAAA
Found at i:36935 original size:2 final size:2
Alignment explanation
Indices: 36928--36965 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
36918 TCTTTTAGTG
*
36928 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36966 CTACGGAGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:37063 original size:15 final size:16
Alignment explanation
Indices: 37028--37087 Score: 86
Period size: 16 Copynumber: 3.8 Consensus size: 16
37018 ATTAGGCGGG
*
37028 TTCGGCTTCGGGTATT
1 TTCGGGTTCGGGTATT
37044 TTCGGGTTCGGGTA-T
1 TTCGGGTTCGGGTATT
*
37059 TTCGGATTCGGGTATT
1 TTCGGGTTCGGGTATT
*
37075 TTCGGGTTGGGGT
1 TTCGGGTTCGGGT
37088 TCGGGTTCGG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
15 14 0.36
16 25 0.64
ACGTcount: A:0.07, C:0.13, G:0.38, T:0.42
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:37063 original size:31 final size:31
Alignment explanation
Indices: 37028--37087 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
37018 ATTAGGCGGG
*
37028 TTCGGCTTCGGGTATTTTCGGGTTCGGGTAT
1 TTCGGATTCGGGTATTTTCGGGTTCGGGTAT
*
37059 TTCGGATTCGGGTATTTTCGGGTTGGGGT
1 TTCGGATTCGGGTATTTTCGGGTTCGGGT
37088 TCGGGTTCGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.07, C:0.13, G:0.38, T:0.42
Consensus pattern (31 bp):
TTCGGATTCGGGTATTTTCGGGTTCGGGTAT
Found at i:37087 original size:6 final size:6
Alignment explanation
Indices: 37075--37140 Score: 75
Period size: 6 Copynumber: 11.5 Consensus size: 6
37065 TTCGGGTATT
* * * *
37075 TTCGGG TTGGGG TTCGGG TTC-GG TCCGGG -TCGGG TCCGGG TCCGGG
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
37121 -TCGGG TTCGGG TTCGGG TTC
1 TTCGGG TTCGGG TTCGGG TTC
37141 ACTTTCGATA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
5 12 0.24
6 39 0.76
ACGTcount: A:0.00, C:0.21, G:0.50, T:0.29
Consensus pattern (6 bp):
TTCGGG
Found at i:37110 original size:11 final size:11
Alignment explanation
Indices: 37096--37138 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
37086 GTTCGGGTTC
37096 GGTCCGGGTCG
1 GGTCCGGGTCG
37107 GGTCCGGGTCCG
1 GGTCCGGGT-CG
37119 GGT-CGGGTTCG
1 GGTCCGGG-TCG
*
37130 GGTTCGGGT
1 GGTCCGGGT
37139 TCACTTTCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.00, C:0.23, G:0.53, T:0.23
Consensus pattern (11 bp):
GGTCCGGGTCG
Found at i:37116 original size:17 final size:17
Alignment explanation
Indices: 37096--37138 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
37086 GTTCGGGTTC
37096 GGTCCGGGTCGGGTCCG
1 GGTCCGGGTCGGGTCCG
*
37113 GGTCCGGGTCGGGTTCG
1 GGTCCGGGTCGGGTCCG
*
37130 GGTTCGGGT
1 GGTCCGGGT
37139 TCACTTTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.00, C:0.23, G:0.53, T:0.23
Consensus pattern (17 bp):
GGTCCGGGTCGGGTCCG
Found at i:37905 original size:16 final size:15
Alignment explanation
Indices: 37884--37926 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
37874 CGGGCTCGGG
37884 TCGGGTTCGGGATGTC
1 TCGGGTTCGGGAT-TC
*
37900 TCGGGTTCGGAGATTT
1 TCGGGTTCGG-GATTC
37916 TCGGGTTCGGG
1 TCGGGTTCGGG
37927 CGGGTTCGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 1 0.04
16 21 0.84
17 3 0.12
ACGTcount: A:0.07, C:0.16, G:0.44, T:0.33
Consensus pattern (15 bp):
TCGGGTTCGGGATTC
Found at i:37988 original size:10 final size:10
Alignment explanation
Indices: 37975--38000 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
37965 ATTTCGGGTT
37975 CGGATTCGGA
1 CGGATTCGGA
37985 CGGATTCGGA
1 CGGATTCGGA
37995 CGGATT
1 CGGATT
38001 TCGAGTTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.23
Consensus pattern (10 bp):
CGGATTCGGA
Found at i:38730 original size:13 final size:13
Alignment explanation
Indices: 38712--38748 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
38702 TTAATTATTA
38712 GGAGGGTCAAATT
1 GGAGGGTCAAATT
*
38725 GGAGGGACAAATT
1 GGAGGGTCAAATT
38738 GGAGGGTCAAA
1 GGAGGGTCAAA
38749 AAGAATTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.41, T:0.16
Consensus pattern (13 bp):
GGAGGGTCAAATT
Found at i:39034 original size:16 final size:16
Alignment explanation
Indices: 39013--39044 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39003 AAATCAAAAA
39013 CTCCAAATTCTTGTGT
1 CTCCAAATTCTTGTGT
*
39029 CTCCAAATTTTTGTGT
1 CTCCAAATTCTTGTGT
39045 TCAATTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.22, G:0.12, T:0.47
Consensus pattern (16 bp):
CTCCAAATTCTTGTGT
Found at i:42041 original size:2 final size:2
Alignment explanation
Indices: 42036--42125 Score: 173
Period size: 2 Copynumber: 45.5 Consensus size: 2
42026 TTAGGGGGGG
42036 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
42078 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G-
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
42119 GA GA GA G
1 GA GA GA G
Statistics
Matches: 87, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 86 0.99
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.